annotate_chip: Annotate "chip.data", given as parameter.

In ArnaudDroitLab/ef.utils: Eric Utilities

Description

Annotate "chip.data", given as parameter.

Usage

annotate_chip(chip.data, input.chrom.state, tf.regions, histone.regions,
  pol.regions, expression.levels, genome.build = c("hg19", "mm9", "mm10",
  "hg38"), biosample = "GM12878", tssRegion = c(-3000, 3000), output.dir,
  label)

Arguments

chip.data	A GRanges object containing the ChIP-seq data.
input.chrom.state	The name of the file containing the information about chromatin states.
tf.regions	A GRangesList object containing the TF regions.
histone.regions	A GRangesList object containing the histone regions.
pol.regions	A GRangesList object containing the pol2 regions.
expression.levels	A data frame containing the levels of expression of genes. according to their EMSEMBL id.
genome.build	The name of the chosen annotation ("hg38", "mm9", "mm10", "hg19").
biosample	The biosample identifier from ENCODE. Valid examples are GM12878, K562.
tssRegion	A vector with the region range to TSS.
output.dir	The name of the directory where to write the selected annotations.
label	The name of the file containing all annotation.

Value

The annotated "chip.data".

ArnaudDroitLab/ef.utils documentation built on Aug. 13, 2019, 9:09 p.m.